Genome Taxonomy Database

The Genome Taxonomy Database (GTDB) is an online database that maintains information on a proposed nomenclature of prokaryotes, following a phylogenomic approach based on a set of conserved single-copy proteins. In addition to resolving paraphyletic groups, this method also reassigns taxonomic ranks algorithmically, updating names in both cases.[1] Information for archaea was added in 2020,[2] along with a species classification based on average nucleotide identity.[3] Each update incorporates new genomes as well as automated and manual curation of the taxonomy.[4]

Genome Taxonomy Database
Content
DescriptionProposed prokaryotic nomenclature
Contact
Research centerAustralian Centre for Ecogenomics, University of Queensland
AuthorsPhil Hugenholtz, Maria Chuvochina, Christian Rinke
Primary citationPMID 30148503
Release date2018
Access
Websitehttps://gtdb.ecogenomic.org/
Miscellaneous
LicenseCC BY-SA 4.0
VersionR07/RS207 (8 April 2022)
Curation policymixed

An open-source tool called GTDB-Tk is available to classify draft genomes into the GTDB hierarchy.[5] The GTDB system, via GTDB-Tk, has been used to catalogue not-yet-named bacteria in the human gut microbiome and other metagenomic sources.[6][7]

The GTDB is incorporated into the Bergey's Manual of Systematics of Archaea and Bacteria in 2019 as its phylogenomic resource.[8]

See also

References
  1. Parks, DH; Chuvochina, M; Waite, DW; Rinke, C; Skarshewski, A; Chaumeil, PA; Hugenholtz, P (November 2018). "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life". Nature Biotechnology. 36 (10): 996–1004. bioRxiv 10.1101/256800. doi:10.1038/nbt.4229. PMID 30148503. S2CID 52093100.
  2. Rinke, Christian; Chuvochina, Maria; Mussig, Aaron J.; Chaumeil, Pierre-Alain; Davín, Adrián A.; Waite, David W.; Whitman, William B.; Parks, Donovan H.; Hugenholtz, Philip (21 June 2021). "A standardized archaeal taxonomy for the Genome Taxonomy Database". Nature Microbiology. 6 (7): 946–959. doi:10.1038/s41564-021-00918-8. ISSN 2058-5276.
  3. Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea". Nature Biotechnology. 38 (9): 1079–1086. bioRxiv 10.1101/771964. doi:10.1038/s41587-020-0501-8. PMID 32341564. S2CID 216560589.
  4. For information on each update, see relevant change logs. For notable, paper-worthy changes, see "Cite GTDB" section on the About page.
  5. Chaumeil, PA; Mussig, AJ; Hugenholtz, P; Parks, DH (15 November 2019). "GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database". Bioinformatics. doi:10.1093/bioinformatics/btz848. PMC 7703759. PMID 31730192.
  6. Almeida, Alexandre; Nayfach, Stephen; Boland, Miguel; Strozzi, Francesco; Beracochea, Martin; Shi, Zhou Jason; Pollard, Katherine S.; Sakharova, Ekaterina; Parks, Donovan H.; Hugenholtz, Philip; Segata, Nicola; Kyrpides, Nikos C.; Finn, Robert D. (20 July 2020). "A unified catalog of 204,938 reference genomes from the human gut microbiome". Nature Biotechnology. doi:10.1038/s41587-020-0603-3. PMC 7801254. PMID 32690973.
  7. Nayfach, Stephen; Roux, Simon; Seshadri, Rekha; Udwary, Daniel; Varghese, Neha; Schulz, Frederik; Wu, Dongying; Paez-Espino, David; Chen, I-Min; Huntemann, Marcel; Palaniappan, Krishna; Ladau, Joshua; Mukherjee, Supratim; Reddy, T. B. K.; Nielsen, Torben; Kirton, Edward; Faria, José P.; Edirisinghe, Janaka N.; Henry, Christopher S.; Jungbluth, Sean P.; Chivian, Dylan; Dehal, Paramvir; Wood-Charlson, Elisha M.; Arkin, Adam P.; Tringe, Susannah G.; Visel, Axel; Woyke, Tanja; Mouncey, Nigel J.; Ivanova, Natalia N.; Kyrpides, Nikos C.; Eloe-Fadrosh, Emiley A. (9 November 2020). "A genomic catalog of Earth's microbiomes". Nature Biotechnology. doi:10.1038/s41587-020-0718-6. PMC 8041624.
  8. "Incorporation of Phylogenomics into BMSAB". Bergey's Manual Trust.
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